Questions

• What is the difference between interwoundand toroidal supercoiling? – Give an example of toroidal supercoiling that

occurs inside the cell.

Supercoiling of DNA

3. DNA compaction requires special form of supercoiling

A. Interwound: supercoiling of DNA in solution

B. Toroidal- tight left handed turns, packing of DNA

both forms are interconvertible

Toroidal

Molecular Cloning:Construction of a recombinant DNA

Molecular Cloning: Cloning Vectors

• Plasmids

Grand-daddy of plasmids

Molecular Cloning: Cloning Vectors

• Plasmids– Origin of replication, determines the

number of copies per cell– Marker genes: ampicillin and tetracycline

resistance genes– Unique restriction enzyme cut sites

Creation of a polylinker or multiple cloning site

Molecular Cloning: Cloning Vectors

1. Plasmids– Origin of replication, determines the

number of copies per cell– Marker genes: ampicillin and tetracycline

resistance genes– Unique restriction enzyme cut sites

• Polylinker of MCS– Small size

• Limitation is ~15,000 bp

Questions

• How many different ways are there to construct recombinant plasmids (hint: try a Google or similar search, also check out Invitrogen)?

Invitrogen's TOPO TA Cloning System (TOPO Cloning)

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications

Figure 2. Gateway® technology facilitates cloning of genes, into and back out of, multiple vectors via site-specific recombination.Once a gene is cloned into an Entry clone you can then move the DNA fragment into one or more destination vectors simultaneously.

Entry of DNA into cells

• Chemical Transformation– Treat cells with calcium chloride– Heat shock

• Electroporation– High voltage transiently makes bacterial

membrane permeable

Special examples of different plasmids

• Expression vectors

What are the considerations in vector construction that need to be taken into account with over-

expression of a protein?

Questions

• Why are protein expression vectors useful?• What kind of cells are proteins generally

over-expressed in and why?• What are the considerations in vector

construction that need to be taken into account with over-expression of a protein?

Special examples of different plasmids

A. Expression vectors– Strong promoter for transcription– Ribosome binding site– Transcription terminator– Some way of controlling gene – making it

inducible

Fusion proteins

Tag expressed protein with another protein or a short peptide

Type of Tags

• Fluorescent proteins– One example is the green fluorescent

protein or GFP

Type of Tags

• Fluorescent proteins– Examples is the green fluoresecent protein

or GFP• Epitope tag

– Short peptide sequence which has an antibody that recognizes it specifically

Type of Tags

• Fluorescent proteins– Examples is the green fluoresecent protein or

GFP• Epitope tag

– Short peptide sequence which has an antibody that recognizes it specifically

• Metal chelator– Can bind to Ni or Co chelated and immobolized

Special examples of different plasmids

B. Shuttle vectors– Contains origins of replication from two different

organisms– Can be replicated in both – Often used to shuttle plasmids from bacteria to

yeastC. Cosmids

- Plasmids containing at least one cos (cohesive-end site) of lambda phage

- Up to 44 kbps

Molecular Cloning: Cloning Vectors

2. Bacteriophages: example is lambda– 1/3 of genome (48.5 Kb) is non essential– DNA is packaged into phage particles– Can only fit 40 – 53 Kb of DNA – Have an in vitro packaging system– Highly efficient at transforming bacteria – Can clone up to 23 Kb of DNA

Molecular Cloning: Cloning Vectors

3. Bacterial Artificial Chromosomes (BAC)– 100 to 300 Kb in size– Have selectable markers– Stable origin of replication– Size of inserts is ~100 KB– Uses electroporation

Molecular Cloning: Cloning Vectors

4. Yeast Artificial Chromosomes

Molecular Cloning: Cloning Vectors

4. Yeast Artificial Chromosomes (YAC)– ARS or origin of replication– Selectable markers– CEN or centromere sequence for proper

segregation– Telomere sequences– Suitable for very large DNAs

A DNA library

• Collection of DNA clones• Source for gene discovery• Largest example is genomic library• Other subsets would be such things as:

– cDNA libraries• Can scan these libraries by DNA

hybridization

• Why are cDNA libraries still so important in the era of genomics?

• What information can be derived from cDNA that are not obtained generally by DNA microarrays?

Full-length cDNA clones and the sequence information derived thereof are the entry to:

• Proteomics : Only full-length cDNAs enable the synthesis, use, and analysis of proteins.

• Gene Regulation : Only full-length cDNAs allow for promoter identification, and as such give you access to the regulatory information that drives gene expression.

• RNAi : The more information you have the greater your chances to prepare a specific RNAi probe.

• Splicing : Only full-length cDNA information can tell you about the true exon composition of transcripts.

• Genomics : Full-length cDNAs are needed for gene discovery and correct mapping of genomic locations.

• SNP Analysis : Only a complete and correct annotation of a gene enables functional characterization of SNPs.

Next time on to protein methods

Change in the syllabus – will not be doing protein structure in this section

Questions

• Why would you need to purify protein?• What properties of proteins can be used to

separate and purify them from each other?• What is column chromatography and how

does it apply to protein purification?• What causes proteins to denature?